Final Fantasy: The Spirits Within is set on an alien-infested Earth in the year 2065. The remaining humans live in "barrier cities" all over the world and attempt to free their planet from the alien race know as the Phantoms. The only hope for the planet comes from the scientist Aki Ross and her mentor Dr. Sid, who have a plan to destroy the Phantoms without damaging the planet, but a general named Hein is determined to use the Zeus space cannon to destory the Phantoms -- even if it means destroying the Earth in the process.

The film was neither a critical nor a popular success. Its plot was typically Japanese and did not appeal to mainstream Western audiences, although it seemed to be better received by regular viewers of anime, who had more experience with Eastern conventions of storytelling. (In some respects Final Fantasy: The Spirits Within was no more and no less than a big-budget anime.) Poor box office, combined with the astronomical cost of production, essentially bankrupted Square Pictures[?], the Squaresoft spin-off that produced it, although Square did survive long enough to produce an animated tie-in to The Matrix,Final Flight of the Osiris. This short film showed additional refinements to Square's virtual actors.